Personal tools

Coexpression cluster:C377

From FANTOM5_SSTAR

Revision as of 19:26, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C377_pituitary_small_smallcell_cerebellum_pineal_pons_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr17:27382155..27382164,+p@chr17:27382155..27382164
+
Hg19::chr20:5892147..5892163,+p1@CHGB
Hg19::chr20:5897502..5897528,+p@chr20:5897502..5897528
+
Hg19::chr20:5903109..5903130,+p@chr20:5903109..5903130
+
Hg19::chr20:5903160..5903179,+p@chr20:5903160..5903179
+
Hg19::chr20:5903185..5903220,+p@chr20:5903185..5903220
+
Hg19::chr20:5903291..5903312,-p@chr20:5903291..5903312
-
Hg19::chr20:5903294..5903305,+p@chr20:5903294..5903305
+
Hg19::chr20:5903323..5903338,+p@chr20:5903323..5903338
+
Hg19::chr20:5903421..5903428,+p@chr20:5903421..5903428
+
Hg19::chr20:5903426..5903436,-p@chr20:5903426..5903436
-
Hg19::chr20:5903492..5903502,-p@chr20:5903492..5903502
-
Hg19::chr20:5903646..5903656,+p@chr20:5903646..5903656
+
Hg19::chr20:5903694..5903708,+p@chr20:5903694..5903708
+
Hg19::chr20:5903713..5903737,+p@chr20:5903713..5903737
+
Hg19::chr20:5903751..5903780,+p@chr20:5903751..5903780
+
Hg19::chr20:5903783..5903796,+p@chr20:5903783..5903796
+
Hg19::chr20:5903825..5903912,+p@chr20:5903825..5903912
+
Hg19::chr20:5903888..5903912,-p@chr20:5903888..5903912
-
Hg19::chr20:5903937..5903949,+p@chr20:5903937..5903949
+
Hg19::chr20:5903983..5904030,-p@chr20:5903983..5904030
-
Hg19::chr20:5904015..5904025,+p@chr20:5904015..5904025
+
Hg19::chr20:5904046..5904073,-p@chr20:5904046..5904073
-
Hg19::chr20:5904056..5904076,+p@chr20:5904056..5904076
+
Hg19::chr20:5904110..5904121,+p@chr20:5904110..5904121
+
Hg19::chr20:5904190..5904198,+p@chr20:5904190..5904198
+
Hg19::chr20:5904275..5904286,+p@chr20:5904275..5904286
+
Hg19::chr20:5904344..5904383,+p@chr20:5904344..5904383
+
Hg19::chr2:166529664..166529668,+p@chr2:166529664..166529668
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism6.30e-42115
central nervous system1.95e-3982
regional part of nervous system2.52e-3994
nervous system2.52e-3994
neural tube5.25e-3657
neural rod5.25e-3657
future spinal cord5.25e-3657
neural keel5.25e-3657
brain5.31e-3269
future brain5.31e-3269
regional part of brain4.69e-3059
neurectoderm6.81e-2990
neural plate4.11e-2886
presumptive neural plate4.11e-2886
regional part of forebrain4.97e-2841
forebrain4.97e-2841
future forebrain4.97e-2841
anterior neural tube7.01e-2742
ectoderm1.43e-23173
presumptive ectoderm1.43e-23173
gray matter7.38e-2334
brain grey matter7.38e-2334
ectoderm-derived structure1.08e-22169
telencephalon1.12e-2234
regional part of telencephalon6.31e-2233
cerebral hemisphere1.50e-2132
anterior region of body1.75e-19129
craniocervical region1.75e-19129
pre-chordal neural plate4.02e-1961
head9.82e-19123
regional part of cerebral cortex1.83e-1822
neocortex6.81e-1720
cerebral cortex8.17e-1725
pallium8.17e-1725
embryo3.83e-10612
posterior neural tube4.12e-1015
chordal neural plate4.12e-1015
segmental subdivision of nervous system8.77e-0913
embryonic structure1.42e-08605
developing anatomical structure1.42e-08605
multi-tissue structure1.88e-08347
germ layer2.70e-08604
embryonic tissue2.70e-08604
presumptive structure2.70e-08604
epiblast (generic)2.70e-08604
segmental subdivision of hindbrain2.88e-0812
hindbrain2.88e-0812
presumptive hindbrain2.88e-0812
anatomical conduit3.13e-08241
tube4.87e-08194
basal ganglion1.60e-079
nuclear complex of neuraxis1.60e-079
aggregate regional part of brain1.60e-079
collection of basal ganglia1.60e-079
cerebral subcortex1.60e-079
nucleus of brain1.66e-079
neural nucleus1.66e-079
temporal lobe1.67e-077
organ5.17e-07511
diencephalon8.47e-077
future diencephalon8.47e-077


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.